Stand-alone life science training events and e-learning solutions are among the most sought-after modes of training because they address both point-of-need learning and the limited timeframes ...available for "upskilling." Yet, finding relevant life sciences training courses and materials is challenging because such resources are not marked up for internet searches in a consistent way. This absence of markup standards to facilitate discovery, re-use, and aggregation of training resources limits their usefulness and knowledge translation potential. Through a joint effort between the Global Organisation for Bioinformatics Learning, Education and Training (GOBLET), the Bioschemas Training community, and the ELIXIR FAIR Training Focus Group, a set of Bioschemas Training profiles has been developed, published, and implemented for life sciences training courses and materials. Here, we describe our development approach and methods, which were based on the Bioschemas model, and present the results for the 3 Bioschemas Training profiles: TrainingMaterial, Course, and CourseInstance. Several implementation challenges were encountered, which we discuss alongside potential solutions. Over time, continued implementation of these Bioschemas Training profiles by training providers will obviate the barriers to skill development, facilitating both the discovery of relevant training events to meet individuals' learning needs, and the discovery and re-use of training and instructional materials.
With the increase of technical and scientific topics, in 2013, PLOS Computational Biology tried a new experience with a similar format—we introduced “Quick Tips” (QT) articles—with the attempt to ...make a clear distinction between the more specific and focused scientific activities and skills presented with resources, databases, and other tools in Quick Tips versus the broader themes presented in a Ten Simple Rules article. ...it is not a Quick Tips but a Ten Simple Rules article. Give tips, not rules Quick Tips are for guiding readers on developing scientific and technical skills on using databases, resources, computational or data analysis methods and tools. ...we recommend Quick Tips authors incorporate a figure summarizing and illustrating their tips (Fig 1).
Abstract
Switzerland has been a pioneer in the field of bioinformatics since the early 1980s. As time passed, the need for one entity to gather and represent bioinformatics on a national scale was ...felt and, in 1998, the SIB Swiss Institute of Bioinformatics was created. Hence, 2018 marks the Institute’s 20th anniversary. Today, the Institute federates 65 research and service groups across the country—whose activity domains range from genomics, proteomics, medicine and health to structural biology, systems biology, phylogeny and evolution—and a group whose sole task is dedicated to training. The Institute hosts 12 competence centres that provide bioinformatics and biocuration expertise to life scientists across the country. SIB sensed early on that the wealth of data produced by modern technologies in medicine and the growing self-awareness of patients was about to revolutionize the way medical data are considered. In 2012, it created a Clinical Bioinformatics group to address the issue of personalized health, thus working towards a more global approach to patient management, and more targeted and effective therapies. In this respect, SIB has a major role in the Swiss Personalized Health Network to make patient-related data available to research throughout the country. The uniqueness of the Institute’s governance structure has also inspired the structure of other European life science organizations, notably ELIXIR.
Bioinformatics tools for proteomics, also called proteome informatics tools, span today a large panel of very diverse applications ranging from simple tools to compare protein amino acid compositions ...to sophisticated software for large‐scale protein structure determination. This review considers the available and ready to use tools that can help end‐users to interpret, validate and generate biological information from their experimental data. It concentrates on bioinformatics tools for 2‐DE analysis, for LC followed by MS analysis, for protein identification by PMF, by peptide fragment fingerprinting and by de novo sequencing and for data quantitation with MS data. It also discloses initiatives that propose to automate the processes of MS analysis and enhance the quality of the obtained results.
...of these changes in medical record keeping, Altman discussed the need for clinical professionals to gain an appreciation of and level of comfort in working with various scales of "big data." ...Since big biological data is also predicted to become big business 29, direct-to-consumer genomics services (e.g., 23andMe) are spending enormous resources on communicating complex scientific data to their web-savvy clients 30.
Background: Biocuration involves a variety of teams and individuals across the globe. However, they may not self-identify as biocurators, as they may be unaware of biocuration as a career path or ...because biocuration is only part of their role. The lack of a clear, up-to-date profile of biocuration creates challenges for organisations like ELIXIR, the ISB and GOBLET to systematically support biocurators and for biocurators themselves to develop their own careers. Therefore, the ELIXIR Training Platform launched an Implementation Study in order to i) identify communities of biocurators, ii) map the type of curation work being done, iii) assess biocuration training, and iv) draw a picture of biocuration career development.
Methods: To achieve the goals of the study, we carried out a global survey on the nature of biocuration work, the tools and resources that are used, training that has been received and additional training needs. To examine these topics in more detail we ran workshop-based discussions at ISB Biocuration Conference 2019 and the ELIXIR All Hands Meeting 2019. We also had guided conversations with selected people from the EMBL-European Bioinformatics Institute.
Results: The study illustrates that biocurators have diverse job titles, are highly skilled, perform a variety of activities and use a wide range of tools and resources. The study emphasises the need for training in programming and coding skills, but also highlights the difficulties curators face in terms of career development and community building.
Conclusion: Biocurators themselves, as well as organisations like ELIXIR, GOBLET and ISB must work together towards structural change to overcome these difficulties. In this article we discuss recommendations to ensure that biocuration as a role is visible and valued, thereby helping biocurators to proceed with their career.
Everything we do today is becoming more and more reliant on the use of computers. The field of biology is no exception; but most biologists receive little or no formal preparation for the ...increasingly computational aspects of their discipline. In consequence, informal training courses are often needed to plug the gaps; and the demand for such training is growing worldwide. To meet this demand, some training programs are being expanded, and new ones are being developed. Key to both scenarios is the creation of new course materials. Rather than starting from scratch, however, it's sometimes possible to repurpose materials that already exist. Yet finding suitable materials online can be difficult: They're often widely scattered across the internet or hidden in their home institutions, with no systematic way to find them. This is a common problem for all digital objects. The scientific community has attempted to address this issue by developing a set of rules (which have been called the Findable, Accessible, Interoperable and Reusable FAIR principles) to make such objects more findable and reusable. Here, we show how to apply these rules to help make training materials easier to find, (re)use, and adapt, for the benefit of all.
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